Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1

The RNA binding protein Celf1 regulates alternative splicing in the nucleus and mRNA stability and translation in the cytoplasm. Celf1 is strongly down-regulated during mouse postnatal heart development. Its re-induction in adults induced severe heart failure and reversion to fetal splicing and gene expression patterns. However, the impact of Celf1 depletion on cardiac transcriptional and posttranscriptional dynamics in neonates has not been addressed. We found that homozygous Celf1 knock-out neonates exhibited cardiac dysfunction not observed in older homozygous animals, although homozygous mice are smaller than wild type littermates throughout development. RNA-sequencing of mRNA from homozygous neonatal hearts identified a network of cell cycle genes significantly up-regulated and down-regulation of ion transport and circadian genes. Cell cycle genes are enriched for Celf1 binding sites supporting a regulatory role in mRNA stability of these transcripts. We also identified a cardiac splicing network coordinated by Celf1 depletion. Target events contain multiple Celf1 binding sites and enrichment in GU-rich motifs. Identification of direct Celf1 targets will advance our knowledge in the mechanisms behind developmental networks regulated by Celf1 and diseases where Celf1 is mis-regulated. RNA-seq was performed in RNA samples of cardiac ventricles at postnatal day 3 (PN3) and at postnatal day 38 (PN38) from wild type mice or Celf1 knock out mice (homozygous)RNA结合蛋白Celf1可在细胞核内调控可变剪接，在细胞质中调控mRNA稳定性与翻译过程。在小鼠出生后心脏发育进程中，Celf1的表达水平显著下调。向成年小鼠体内重新诱导Celf1表达，会引发严重心力衰竭，并使基因表达与可变剪接模式恢复至胎儿阶段。然而，目前尚未明确Celf1缺失对新生小鼠心脏转录及转录后调控动态的影响。 本研究发现，纯合Celf1敲除的新生小鼠会出现心脏功能障碍，而该表型在纯合敲除的成年小鼠中并未观察到；尽管在整个发育阶段，纯合敲除小鼠的体型均小于野生型同窝仔鼠。对纯合敲除新生小鼠的心脏mRNA开展RNA测序（RNA-sequencing）分析后发现，细胞周期相关基因的表达网络出现显著上调，而离子转运与昼夜节律相关基因则呈现下调趋势。细胞周期基因富集有Celf1结合位点，这佐证了Celf1对这类转录本的mRNA稳定性具有调控作用。本研究还鉴定出了由Celf1缺失所调控的心脏可变剪接网络，其靶标事件包含多个Celf1结合位点，且显著富集GU富集基序。 鉴定Celf1的直接靶标，将有助于深化我们对Celf1调控的发育网络以及Celf1表达失调相关疾病发病机制的认知。本研究针对野生型小鼠与纯合Celf1敲除小鼠，分别采集其出生后第3天（PN3）和出生后第38天（PN38）的心脏心室RNA样本，开展了RNA测序实验。